TY - GEN
T1 - Transcriptome analysis of HIV-1 virus in understanding the effect of antiretroviral drugs (cART) and methamphetamine on the virus
AU - Thapa, Shwor
AU - Fox, Oward S.
AU - Bastola, Hundy R.
N1 - Funding Information:
This work was supported by NIH grants P30 MH062261 and ROI DA030962 and its content is solely the responsibility of the authors and does not necessarily represent the official views of NIH.
Publisher Copyright:
© 2015 IEEE.
PY - 2015/12/16
Y1 - 2015/12/16
N2 - The use of methamphetamine and infection of HIV are both considered public health issues by the Centers of Disease Control and Prevention (CDC). Many studies have shown the effect of methamphetamine, HIV, and both to the central nervous system. The use of methamphetamine not only increases the tendency of HIV transmission, but also the severity of the infection, which may lead to neurodegeneration and neurocognitive disorders. Several studies have examined the gene expression changes in the host due to viral infection, antiretroviral treatment, and the use of methamphetamine, but there is a lack of understanding of their impact on the virus. We investigated their effect on the HIV-1 virus by analyzing the amount of reads obtained from RNA sequencing. We showed that the use of antiretroviral drugs reduced viral read levels, whereas methamphetamine increased them. The expression level of some of the HIV-1 genes such as gag, pol, and nef, inferred from the count of reads mapped to their genomic locations, showed different temporal states among our biological samples.
AB - The use of methamphetamine and infection of HIV are both considered public health issues by the Centers of Disease Control and Prevention (CDC). Many studies have shown the effect of methamphetamine, HIV, and both to the central nervous system. The use of methamphetamine not only increases the tendency of HIV transmission, but also the severity of the infection, which may lead to neurodegeneration and neurocognitive disorders. Several studies have examined the gene expression changes in the host due to viral infection, antiretroviral treatment, and the use of methamphetamine, but there is a lack of understanding of their impact on the virus. We investigated their effect on the HIV-1 virus by analyzing the amount of reads obtained from RNA sequencing. We showed that the use of antiretroviral drugs reduced viral read levels, whereas methamphetamine increased them. The expression level of some of the HIV-1 genes such as gag, pol, and nef, inferred from the count of reads mapped to their genomic locations, showed different temporal states among our biological samples.
KW - HIV-1
KW - Methamphetamine
KW - RNA-Seq
KW - antiretroviral drugs (cART)
KW - transcriptome
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U2 - 10.1109/BIBM.2015.7359813
DO - 10.1109/BIBM.2015.7359813
M3 - Conference contribution
AN - SCOPUS:84962361519
T3 - Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015
SP - 962
EP - 968
BT - Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015
A2 - Schapranow, lng. Matthieu
A2 - Zhou, Jiayu
A2 - Hu, Xiaohua Tony
A2 - Ma, Bin
A2 - Rajasekaran, Sanguthevar
A2 - Miyano, Satoru
A2 - Yoo, Illhoi
A2 - Pierce, Brian
A2 - Shehu, Amarda
A2 - Gombar, Vijay K.
A2 - Chen, Brian
A2 - Pai, Vinay
A2 - Huan, Jun
PB - Institute of Electrical and Electronics Engineers Inc.
T2 - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015
Y2 - 9 November 2015 through 12 November 2015
ER -